RetrogeneDB ID: | retro_ecab_70 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 14:62789984..62790635(-) | ||
| Located in intron of: | ENSECAG00000011896 | ||
Retrocopy information | Ensembl ID: | ENSECAG00000002023 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SOD2 | ||
| Ensembl ID: | ENSECAG00000011797 | ||
| Aliases: | SOD2, Mn-SOD | ||
| Description: | superoxide dismutase [Source:RefSeq peptide;Acc:NP_001075986] |
Retrocopy-Parental alignment summary:
>retro_ecab_70
ATGTTGTGCCGGGCGGAGTGCAGCACGAGCAGGAAGCTGGTGCCAGCTCTGGGGTCCCAGCAGAAGCACAGCCTCCCCGA
CTTGCAGTATGATTATGGCACCCTGGAGCCCTACATCAATGCCCAGATCATGCAGCTGCACCACAGCAAGCACCACGCGG
CCTATGTGAACAACCTGAACGTCACCAAGGAGAAGTACAAGGAGGCGCTGGCCAAGGGGGACGTGACAGCTCAGACTGCT
TTGCAGCCTGCACTGAAGTTCAATGGTGGAGGCCATATCAATCATACCATTTTCTGGACAAACCTGAGCCCCAATGGCGG
GGGAGAACCCAAAGGGCAATTGCGGGACGCCAACTTTGGTTCCTTCGACAAATTTAAACAGAAGTTGACCGCTGTATCGG
CTGGTGTCCAAGGCTCGGGTTGGGGTTGGCTCGGTTTCAATAAGGACCAGGGACGTCTCCAGATTGTTGCCTGTCCTAAC
CAGGATCCCCTGCAGGGAACAACAGGTCTTATTCCCCTGCTGGGGATTGACGTGTGGGAGCACGCTTATTACCTTCAGTA
TAAAAACGTCAGGCCTGATTATCTGAAAGCCATTTGGAATGTGATCAACTGGGAGAATGTATCTGAGAGATACATGGCTT
GCAAAAAGTAA
ORF - retro_ecab_70 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.02 % |
| Parental protein coverage: | 98.62 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | STSRKLVPALGSLGSRQKHSLPDLQYDYGALEPYINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGD |
| STSRKLVPA...LGS.QKHSLPDLQYDYG.LEPYINAQIMQLHHSKHHAAYVNNLNVT.EKY.EALAKGD | |
| Retrocopy | STSRKLVPA---LGSQQKHSLPDLQYDYGTLEPYINAQIMQLHHSKHHAAYVNNLNVTKEKYKEALAKGD |
| Parental | VTAQIALQPALKFNGGGHINHTIFWTNLSPNGGGEPKGELLDAIKRDFGSFDKFKEKLTAVSAGVQGSGW |
| VTAQ.ALQPALKFNGGGHINHTIFWTNLSPNGGGEPKG.L.DA....FGSFDKFK.KLTAVSAGVQGSGW | |
| Retrocopy | VTAQTALQPALKFNGGGHINHTIFWTNLSPNGGGEPKGQLRDA---NFGSFDKFKQKLTAVSAGVQGSGW |
| Parental | GWLGFNKDQGRLQIVACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVSERY |
| GWLGFNKDQGRLQIVACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVSERY | |
| Retrocopy | GWLGFNKDQGRLQIVACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVSERY |
| Parental | MACKK |
| MACKK | |
| Retrocopy | MACKK |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP021940_articular_cartilage | 2 .66 RPM | 63 .69 RPM |
| SRP021940_cerebellum | 2 .44 RPM | 34 .90 RPM |
| SRP021940_embryo | 0 .77 RPM | 13 .94 RPM |
| SRP021940_placental_villous | 2 .17 RPM | 53 .60 RPM |
| SRP021940_synovial_membrane | 5 .11 RPM | 112 .77 RPM |
| SRP021940_testis | 1 .09 RPM | 12 .53 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_70 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_70 was not experimentally validated.